Beacons
by LissaUnderground
Summary: Mutant rights are disappearing into the woodwork, and the government still searches for the '97 Queens bomber. As if she didn't have enough on her plate, doctoral candidate and mutant activist, Rory, searches for a beacon, and as an unregistered mutant has piqued the interest of SHIELD. May change to M. Xover with X-Men, and possible others. Starts before the Avengers.
1. Prelude Part 1: Blackened Skies

**A/N: Hi readers! If you opened this up, I'm glad you're giving this a chance. It's been a brain child of mine for almost a year, but I've finally gotten over a horrible writer's block, and hope to turn this into something substantial and fun. I apologize for the eh-ish summary, but I hope to entertain you all. It'll start off slow, and it'll be very heavy. I love reviews and critiques, but please make sure they're constructive. I already have the second half of the prelude done, and have started chapter one. Happy reading!  
**

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**May 17th, 1997: Fresh Meadows, Queens**

It happened so quickly.

Like lightning in a thunderstorm, the sphere of pure energy had pulsed outward, completely destroying homes in an 10 block radius. It was only after smoke began to engulf Fresh Meadows that the earth-shattering boom could be heard, even out on Roosevelt Island.

The smoke mushroomed, billowing so high that it was visible from Jersey.

Traffic came to a halt across New York parkways, a mix of tremors, and the awe and horror. Fresh Meadows was a mess of smoke and ash.

It would take three days to find survivors under the destroyed eastern sector of Fresh Meadows. However, it was approximately four hours into the initial search that newly recruited firefighter Joey Lucas found a little girl, safely shielded by an overturned, scorched, Honda Civic hatchback, nestled where the trunk was, though the trunk's door was long lost. She had a long cut running straight across her forehead, blood leaking over her entire face, and her knees and palms were cut. Somehow, the little girl had survived, when no other survivors could be found in a two block radius of where she was, which was incredible close to where the blast seemed to come from.

She seemed like a miracle amongst chaos, a messiah at world's end, though her cries told a different story.

"Mommy? Fee?" The little girl babbled, eyes welling with tears that left clean, pale streaks of flesh across her bloody face.

Scooping her into his arms, Lucas tried to sooth her. "Sweetheart, you're okay. We'll find you your family." The firefighter spoke softly, hugging her firmly against him, his heart raced in tandem with hers, his pity of her condition controlling him.

He tried to coax her, but she continued to sob out "Mommy? Fee?" over and over, as she was hauled to an ambulance.

He stayed with her as they rode to North Shore Hospital, her intelligent jade green eyes haunting him as if they were filled with ghosts.

"RORY?"

Lucas' head snapped towards the door, as he sat in the hospital room where the young girl was placed. Caroline Masters, age 5, third grader.

The door opened, revealing a man in his late 30s. He stood in the doorway, staring at the child's unexpectedly stable condition. He breathed for a fraction of a second, and then rushed to her side.

"Oh sweetheart, my girl, my baby girl" he choked back a sob, kneeling next to the young girl, kissing her forehead, running her fingers of her blood-matted blonde bangs.

"_Sir," _a nurse stood in the doorway, hair askew. She looked like she didn't know whether to glare and snap, or cry.

Lucas stood up, signaling for her to let it go.

The firefighter and the man, Jack Masters, father of Caroline, shared words, before the former gave him a few moments alone with his child.

He held one of her tiny hands in both of his.

He sat contemplatively for hours, clutching his young daughter, whose mouth was clad in an oxygen mask.

"Daddy."

His head snapped toward her face. Her eyes were open.

"I'm sorry," she cried out.

"No, no baby, there's nothing to be sorry about, you're okay. You're okay." He soothed, but she shook her head erratically as her heartbeat picked up.

"I tried to save them daddy, I swear."

"Baby, you can't save anyone from a bomb."

"But it was Fee daddy."

He froze.

"-she got so mad at mommy, and I tried to raise my shield like mommy told me, but Fee made the lights go out. And then everything was burnings and smoky and I was tossed and couldn't find them," she shook as she relayed the recent memory. Jack stilled, a chill creeping up his spine. He realized that his wife and daughter were gone.

And worse than that, one of his babies was now in danger.

"Sweetie. Rory look at me. Sweetie," he whispered with emphasis, and jade green eyes finally met identical ones. "Ror, you can't tell anyone this. Okay? No one can know what you think you saw."

Caroline nodded twice, eyes wide. Unadulterated fear stood in her father's kind eyes. They would haunt her, just as hers would haunt Joey Lucas'.

Because both green sets held hidden knowledge, and fear for the future.


	2. Prelude Part 2: Flickering Light

**A/N: Okay I was a _bit_ eager to post the second half of the prelude after getting any traffic at all. Thank you to my followers and subscribers, for making me excited to share this second chapter! I probably won't get to post the next next chapter until next weekend, or next Monday, since my schedule is packed as school is winding down. Please review and such, and enjoy :)**

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**May 17th, 2011: Bayside Arcadia Cemetery, Queens **

Michael was the first to lay a lily on the graves. Then it was Jo, then Garrett and then lastly, Jeremy, who had stilled for a few moments before approaching his mother and sister's graves.

_Here lies_

_Cordelia Wesley-Masters_

_Beloved mother, sister, wife, and god-sister_

_11/24/65 – 05/17/97_

_x_

_Here lies_

_Felicia Anne Masters_

_Beloved daughter and sister_

_01/30/88 – 05/17/97_

_x_

Finally he approached them, dropping the flowers to the dirt. He bent down, and picked up two fair-sized stones, and placed one on each of the tombstones. It was a custom he had learned from his girlfriend Rachel; Jews honored their dead loved ones with stones. She once jokingly said that it was because flowers were for the living, though he knew it (thanks to Google) was to make certain that the soul could remain at peace. And anyway, the flowers would die, but the stone would remain. A constant guardian over their tombs. At least until cleaned off by one of the cemetery's groundskeepers. He stepped back.

The final person stayed in place, behind her family. Behind her aunt, older brother, and younger ones. They looked to her. Her eyes were glazed and focused all at once, narrowed as they darted across line, memorizing every groove in the tombstones.

"Rory," Jo said softly.

Caroline ignored her. Her eyes trained on the 'x's marked at the bottom of the graves. Neither of her paternal grandparents had them on their graves, though she recalled that her maternal grandfather had one marked on, though he was located at the family cemetery in Maine. Her father wouldn't have an 'x' on his grave, and neither would her siblings. Or her aunt. But she would.

It was a silent tribute to mutants, something small, but efficient. The 'x's were smaller than the rest of the text, and if you weren't looking for it, perhaps you wouldn't notice it. But of course, all the Master's family knew it well.

She eventually approached her dead big sister and mother's graves, but like Jer, did not place flowers there, nor did she a rock. She simply rested her hands on the graves, and closed her eyes.

Finally she let go, and turned on her heel, surprisingly graceful for 4 inch heels, sinking into moist dirt, and walked away. Her family trailed after her.

As they approached the family 4 seater, a busted, old, green Toyota, Caroline was stopped by her younger brothers's voice.

"Rory?" Caroline turned to look at her 15 year old brother.

"Yeah Mikey?"

"Are you coming home? We're going to drive by the memorial parade." His voice pleaded. She shut her eyes.

"I'm sorry buddy, I have work to do in the lab, really early. I promise I'll come home this weekend."

She hastily swept her younger brother into a hug. He was getting taller; soon he would engulf her 5'7". She then awkwardly hugged Garrett, who was stiff and stoney as ever, a normal rebellious 16 year old.

_Normal, _her mind echoed the word with longing, it reverberating like wind chimes in a heavy breeze.

She then hugged her aunt, who had serious stress lines. Her beautiful brown hair was graying on the sides of her loose bun, and her skinny stature seemed weakened by the stress of time.

Jeremy followed the same line of goodbyes that Caroline gave.

"I'll drive you into the city."

After final goodbyes, the two slid into his sleeker car, a 2 year old Lexus. Jeremy turned onto a highway, them going at 50 down the unbusy road towards the Midtown Tunnel.

"How's dad?" Caroline broke the verbal silence, though some 90's station played softly.

"Didn't you just see him the other day?"

"Yeah but he always puts on a facade with me. He's scared he'll send me off a deep end or some shit. He treats me like I'm made of glass. But I'm not Fee."

"I know."

"I'm nothing like her."

"He knows that."

"You were there when Xavier told him, right? It's why he didn't send me away. What-"

"Ror," Jeremy interrupted her. "He hasn't said anything because of all the stress you're under. I mean for fuck's sake, you just finished your first year towards your doctorate, and you're 19. And you've convinced yourself, that on top of all the work you do for school, you need to take on not just one job, but _two-"_

"How is any of this relevant?"

"-and that's other than the fact that you TA and are doing all of that lab work, and still make the time to go home to help out. And it's relevant because it's amazing you haven't gone insane yet. I mean really, Rory. You skipped, what, 3 grades? Who the hell goes into college when their 15? And even though you got a damn full ride, you still think you need to contribute to paying for dad's hospital bills, when I've been covering everything, and I'm the only person who's made a freaking dent in the family accounts. You're so stressed and stretching yourself so far and thin-"

The music went off.

"Please don't do that."

Caroline looked bored. "Do what?"

"Your... thing-"

"It's called _telekinisis, _Jer."

" I know, and there's nothing wrong with... using it or anything – I don't want you to feel stifled-"

"I'm not _stifled_ Jer-"

"-because you can use your abilities around me, but remember you're-"

"-unregistered, I _know _Jer-"

"-**Don't say it out loud. **And anyway, your fingers are literally inches from the dial."

"Stop changing the subject."

"Huh?"

"How. Is. Dad?"

The car came to an appropriate stop, finally hitting traffic at the toll booths before the tunnel.

"Ugh, why did I leave the EZ Pass at home..."

"_Jer,"_ Caroline's voice dropped almost to a growl. He became silent, tapping the steering wheel. He shut his eyes for a millisecond, exhaling lowly before cracking an eye in his younger sister's direction. He looked away, both hands gripping the wheel, his eyes looking ahead. The traffic moved a few feet as a car went past the booth. He moved before stopping.

And then moved again before stopping.

_Moving._

"He's not getting any better. The doctor's are saying he's "_stably in the lower sector of Stage 3_," which really isn't fucking stable at all."

"Is he going to be getting treatment again?"

"The chemo will start up again."

"Can we afford it?"

"We can't afford not to," he responded firmly.

Caroline silently agreed.

They got past the toll booth, and made their way onto the city streets.

"Let me off at 40th and Park."

"I can drive you uptown."

"It's fine Jer. I really want to walk. I need to breath."

Jer looked at her. He nodded, and made a right turn onto a side street, then twisted his way to their destination. He stopped the car behind a taxi. A doorman came to open the door, but moved away when seeing the unfamiliar passenger.

"Love you."

"I love you too."

"I know."

"If you need anything you should call me."

"I will."

"You say you will, but you never do."

"I don't need anything."

"Rory-"

"Don't." They reached an awkward silence. She looked at her watch, before unbuckling her seat belt. "I'll come by this weekend okay? We can go home together to visit dad."

"Sounds good – you sure you don't want a ride? Columbia's not that far, only 70 blocks."

Caroline snorted.

"Thanks, but no thanks. We both know 3 miles in Manhattan, back and forth – so 6 really – could take you two hours to navigate at this hour. Go home, call Rach. I'll walk to Time Square and grab the E, laugh at the tourist frenzy."

Jeremy looked at his baby sister again. He nodded. The two hugged.

"Be safe."

"Same to you," Rory got out, teetering as she stepped onto the curb, her arms out like a gymnast on a balance beam, before she righted herself. She shut the door, and waited expectantly for him to drive off. He rolled down the window.

"Call me."

"Night Jer," she waved, and walked off, west-side bound.

* * *

Time Square was quickly falling into a greater frenzy than usual, Rory noted. Horns honked loudly as unmarked black cars screeched to a halt in Duffy Square, ignoring all traffic laws. She jumped out of the way, and her ponytail hit her face from the quick wind the car created. In a few seconds, she was practically knocked over by a man in khakis and a white tee, who ran with purpose and amazing speed. Her shoulder stung from the force of his shoulder into hers, yet her eyes were attracted to his racing figure. He ran into the square, and was immediately cornered by cars, and cops began to crowd the scene, trying to disperse crowds. A distant "_at ease_," was heard, but Rory immediately drew focus to two late-arriving cars, as nondescript as all the others. They were skidding into each other at an alarming speed, thanks to the wet ground and unexplained urgency, and they would easily in turn hit the other cars, and most definitely injure all the civilians peering in at what ever the hell was going on.

Without think Rory raised both hands toward the cars, them skidding to halt inches from each other, then pressing back a good three yards.

Realizing what she had done, in public, she began to run off in the direction which she had came, knocking into a brunette man in a suit with a receding hairline and tinted shades. She didn't apologize as she ran off, newly graceful in her heels, in her urgency.

And though he was called by another agent at the scene to go to his director, Agent Phil Coulson stared after the woman with the quick abilities, who hurried off as soon as she appeared.


	3. Chapter 1: Muted Flames

A/N: Hey guys. I apologize for the super late update. Dealing with finals and such. But here it is! I hope you all enjoy, and please review so I can know what you guys think about what you're reading. Thank you and enjoy.

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**March 9th, 2012: Uptown C Platform at 14th Street Station, Manhattan**

If you were to grab a handful of New Yorkers by the shoulders, you'd hear a handful of opinions about the Subway system. Some love, some hate, some hate it for the people, the smell, the peddlers… And some love it for it's bizarre culture.

But it seemed like a New York-universal opinion that the C train was, and still is, the worst train the the New York City transit system. Yes, even worse than the 6 at rush hour.

On this particular night, 1:30 a.m. specifically, Caroline, dressed in a faded blue and white waitress outfit and a black peacoat, and carrying a backpack that, without the added mass of the tote on her left shoulder, swallowed her willowy body, clamored on just before the doors closed at 14th street. She strategically took up a corner double seater, her body stretched on a diagonal, a protective layer for her turtle shell of a backpack, along with the tote, which had her normal clothes in it.

Of course, she hardly stood out, one exhausted college student who clearly just finished her second job, and now had to trek back to her college dorm. She sat amongst others with red rimmed eyes, though from the way that one _gentleman_ with the jeans pulled past their boxers was twitching, it was easy to assume his eyes were a result of something other than tiredness and stress.

She had been waiting on the platform for 20 minutes, and had resorted to changing out of her low heels into her Doctor Scholl's flats. On top of exhaustion and irritation, she was in pain from the heaviness of her bags and standing in those awful uniform-shoes, and she had an exam on Monday.

She opened her shell-pack, and pulled out a textbook, _MCB for the Common Age,_ which had been sandwiched between _Mutant Studies: X-Genes vs. Non-X-Mutations, _and a stack of ungraded exams_. _She began to leaf through it, eventually rummaging for _Post-it Note_ strips. Stations passed, their appearances shifting in a wave-pattern, like looking at a landscape through heavy heat. 23rd, 34th, 42nd, 50th, 59th… and at the crux between 59th, Columbus Circle, and 72nd, the train squealed to a halt, and the lights flickered, blackness engulfing the car, and the two that hugged it, only to re-brighten moments later.

People, all who have shifted in the unexpected stop, righted themselves, a drunken girl in hooker heels clamoring to her feet, clutching her boyfriend's shirt-neck, and the possible druggie clutching his head, which he had smacked against a pole. It seemed like the only people in the car who hadn't become skewed in the surprising top were the girl, and a 30-something year old blonde male, with a squarish face and tinted sunglasses.

_Who wears sunglasses on the subway… or this late at night as it is? _she thought.

The lights flickered off again, and then almost immediately glowed again.

"**We're sorry, we're currently delayed due to a disturbance on the train tracks ahead of us. We'll be moving shortly. We're sorry for the inconvenience."**

There was a collective groan that harmonized throughout the entire train. The blonde woman glanced at her watch, her eyes screwing shut. She breathed and exhaled loudly, her thumb and forefinger pinching the top of her nose, before she went back to reading her textbook, her eyes flying across and down paragraphs, flipping pages at an unbelievable rate. One would assume she didn't absorb anything she read, but her eyes were filled with exhausted determination.

They stood at a standstill for 15 minutes. The speakers crackled, before a different voice was emitted, feminine, and non-recorded.

"**We're sorry, there's a disturbance at 86th Street. The train will move as soon as the area is cleared and safe."**

Her watch now read 2:15. Heinous.

She attempted to continue reading, but her mind her began to drift. Her eye were open a fraction of an inch as her mind became lucid. She wasn't sure how much time passed, but the train began to move, it's slow crawl rocking her to sleep.

* * *

_Swarms of people crowded her. Professors, undergraduate students, customers, her boss, Mikey, Jer, Garrett, Aunt Jo, doctors, politicians, paparazzi. They seemed to form a tornado around her. _

"_Rory!"_

"_Caroline!"_

"_Miss Masters!_

"_Miss!"_

"_Ms!"_

"_Hey lady!"_

"_Lady!"_

"Lady!"

Her eyes jutted open. A husky man in a MTA uniform stood before her. His eyes were yellowed, his hair oily, but wore a sympathetic look on his face.

We've all been there.

"End of the line. You need to get off."

Rory's eyes tried to focus, them looking through the window of the train car at the sign jutting out of the subway station's ceiling.

168th street.

6 stops and 52 blocks late.

"Sorry," her voice was filled with a bit back groan, as she shoved the textbook into her bag. Its heaviness had made her legs tingle as she stood, the impression of the impressive textbook marking her thin legs a fleshy pinkish-red. She collected her belongings, almost stumbling out of the car and onto the platform.

Her watch read 3:11. She was supposed to wake up in 3 hours for class.

Rory pondered actually skipping work, as her body seemed unable to hold herself up. She shuffled up the stairs and around, going halfway down to the downtown platform side, before stopping short.

The C rarely runs late nights.

"Fuck."

She stumbled up flights of the stairs, almost leaving the terminal before realizing that she could take the 1 back downtown to school, where her bed waited for her.

She waited another 20 minutes for the train, and time peeled away painfully, like trying to slowly remove a strip for waxing painlessly.

Sluggishly, she drifted from 116th street station to the apartment, one of a few specifically leased for Columbia's graduate students. She climbed 14 flights of stairs to the 7th floor, keys jangling from her fingertips, their twisted melody only giving her a headache.

She felt worse than she had ever felt from a hangover.

Reaching her apartment, a tiny studio, she gave up caring about decency as she flung open the door, just by flicking her eyes. It banged against the wall, the hinges shaking.

_Too hard._

She winced, and opted to close it with her hands, though really, with the music blasting from above, how would anyone hear her?

She dropped her things, and stumbled to her bed, stripping down to her underwear as she went.

Rory meant to change into pajamas, really she did, but her bed just looked so inviting, with all of its ancient mattress-springs-stabbing-her-spin glory. She dropped, face first. With her last moments of awareness, she recalled not remembering to turn the lock before collapsing. As her vision faded, her eyes shifting with her head, eying the lock, 20 feet away. The lock turned effortlessly, clicking to alert her of safety. Her eyes then shuttered to a close, and she drifted.

* * *

**That Same Morning, 4:29 AM: ****One Building Over**

"Sir."

"Yes Agent?"

"I have a report on Masters."

Barton tried to keep his voice straight as he stifled a yawn. He dropped the binoculars to the ground; unnecessary to begin with, they were merely a precaution and possible aid. They fell to the ground, bouncing lightly off the side, and knocked over onto the _Subway_ wrapper, which had pieces of iceberg lettuce and marinara sauce still stuck to it. the binoculars had knocked into a bottle of Arizona iced tea, sending the bottle rolling on the uneven floor to the other end of the room.

"Report then."

Barton turned away from the window, which gave a perfect view of an apartment on the 7th floor of the neighboring building, and slunk to the floor, his fingers running over the cover of the file next to him.

Filed: Agent Coulson

Updated: Agent Barton

Subject: Caroline J. Masters

Recruitment Assessment

"Subject has displayed small representation of earlier presumed abilities. Locked apartment door while being 7 yards from it. Lends proof to suspected telekinetic abilities, supporting suspicions put in place on May 17th of last year, the day of the Rogers incident and first day of his integration. Other proofs are noted in the file, as they have been reoccurring since October 23rd of last year."

"'Reoccurring' is not a word, Agent."

"Bite me, Phil." Clint puts a hand to his brow as he closes his eyes, jealous of Caroline J. Masters (or as her family called her: _Rory _- which made her sound like she was supposed to be a character on _Gilmore Girls_, because really, how do you get 'Rory' from 'Caroline'?), who is finally getting sleep, while he continues to be deprived of it. Phil Coulson's laugh emits tiredly through the receiver.

"What is your opinion of the subjects eligibility?"

"The evidence is slight, but we've gotten countless occurrences on hand. She's unregistered, but her family is clean in background."

"We might've found information on her through a private server."

Barton's eyebrow raises, while his eyes remain shut.

"Really?"

"An Xavier Institute. They've appeared on our radar before, seemingly benign but useful. They'll be looked into when needed."

"And does it help our case?"

"Exponentially. If what is documented is true, she'd be a beneficial asset."

"If this is known why am I still here, prepared to spend little to no time sleeping on a musty mattress instead of being back in my own apartment - or at least doing a more adventurous task than trailing some college chick?"

"We'll be moving in shortly. Continue shadowing her for the time being. Assets should be protected. She's not just 'some college chick.'"

"Roger that - wait, now that Rogers is in our system, does 'Roger' make things more complicated? Should I be more simplistic like 'got it?' Or should I go more Hollywood and be like 'over and out'?"

"Goodnight Agent."

"Serious questions here Phil."

"You need sleep Clint."

"By the sound of it, you do too, old man." He chided back, hearing a low yawn on the other end - making him want to yawn himself.

"Goodnight."

"Yeah," - click - "night Phil."

Having been hung up on, Barton stood up, shuffling over to the not-as-musty-as-he-described mattress, shedding clothes as he went. Collapsing, much as his stalkee had about 15 minutes ago, he propped himself up barely, as he scrolled to set an alarm.

"Three hours of sleep. Awesome." He mumbled, his eyes shifting to the empty pile of Redbull cans. Trailing overworked night-owls was _the best._

He could only imagine what a piece of work she would be as a teammate, and Caroline J. Masters was his last thought as he fell asleep for a short snooze, just as she seemed to take up all of his time lately.

He fell asleep with a smile on his face, thinking of all the pranks he'd do to get back at her for these on-and-off trying weeks as he shadowed her, once they worked together.

Because of course, S.H.I.E.L.D always gets what they want.

* * *

A/N: Yess, finally an update done. This chapter was initally longer, and much of the ending of this one didn't exist, but I've been a bit stuck with the next part, and what I did have of the last part of this was lost when OpenOffice shut down. So this was born! I hope you enjoyed. Since I have at least a third of the next chapter done, it might actually be done by next weekend (last week of my senior year of high school, bring it on). Please review, and I'll see you guys next update.


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